You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Yeast Metabolome Database.

4-amino-2-methyl-5-diphosphomethylpyrimidine (YMDB00117)

Identification
YMDB IDYMDB00117
Name4-amino-2-methyl-5-diphosphomethylpyrimidine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Description4-amino-2-methyl-5-diphosphomethylpyrimidine, also known as (4-amino-2-methylpyrimidin-5-yl)methyl diphosphate, belongs to the class of organic compounds known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O. 4-amino-2-methyl-5-diphosphomethylpyrimidine is a very strong basic compound (based on its pKa). 4-amino-2-methyl-5-diphosphomethylpyrimidine may be a unique S. cerevisiae (yeast) metabolite.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • (4-amino-2-methylpyrimidin-5-yl)methyl diphosphate
  • 2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate
  • 4-Amino-2-methyl-5-diphosphomethylpyrimidine
  • 4-Amino-2-methyl-5-(diphosphooxymethyl)pyrimidine
  • (4-Amino-2-methylpyrimidin-5-yl)methyl diphosphoric acid
  • 2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphoric acid
CAS numberNot Available
WeightAverage: 299.115
Monoisotopic: 299.007222745
InChI KeyAGQJQCFEPUVXNK-UHFFFAOYSA-N
InChIInChI=1S/C6H11N3O7P2/c1-4-8-2-5(6(7)9-4)3-15-18(13,14)16-17(10,11)12/h2H,3H2,1H3,(H,13,14)(H2,7,8,9)(H2,10,11,12)
IUPAC Name({hydroxy[(6-imino-2-methyl-1,6-dihydropyrimidin-5-yl)methoxy]phosphoryl}oxy)phosphonic acid
Traditional IUPAC Name[hydroxy((4-imino-2-methyl-3H-pyrimidin-5-yl)methoxy)phosphoryl]oxyphosphonic acid
Chemical FormulaC6H11N3O7P2
SMILESCC1=NC=C(COP(O)(=O)OP(O)(O)=O)C(N)=N1
Chemical Taxonomy
Description belongs to the class of organic compounds known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganic oxoanionic compounds
Sub ClassOrganic pyrophosphates
Direct ParentOrganic pyrophosphates
Alternative Parents
Substituents
  • Organic pyrophosphate
  • Aminopyrimidine
  • Monoalkyl phosphate
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Pyrimidine
  • Alkyl phosphate
  • Imidolactam
  • Heteroaromatic compound
  • Azacycle
  • Organoheterocyclic compound
  • Amine
  • Primary amine
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateNot Available
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility6.42 g/LALOGPS
logP-0.59ALOGPS
logP-2.4ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)2.61ChemAxon
pKa (Strongest Basic)1.71ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area161.53 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity69.7 m³·mol⁻¹ChemAxon
Polarizability23.48 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Vitamin B1/Thiamine metabolismPW002486 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Thiamine metabolismec00730 Map00730
SMPDB Reactions
4-amino-2-methyl-5-diphosphomethylpyrimidine + 2-((2R,5Z)-2-Carboxy-4-methylthiazol-5(2H)-ylidene)ethyl phosphate + hydron → Thiamine monophosphate + Carbon dioxide + diphosphate
Pyridoxal 5'-phosphate → 4-amino-2-methyl-5-diphosphomethylpyrimidine
Adenosine triphosphate + 4-amino-2-methyl-5-phosphomethylpyrimidine → ADP + 4-amino-2-methyl-5-diphosphomethylpyrimidine
4-amino-2-methyl-5-diphosphomethylpyrimidine + hydron + 4-methyl-5-(2-phosphonooxyethyl)thiazole → Pyrophosphate + Thiamine monophosphate
KEGG Reactions
4-amino-2-methyl-5-phosphomethylpyrimidine + Adenosine triphosphate → 4-amino-2-methyl-5-diphosphomethylpyrimidine + ADP
4-Methyl-5-(2-phosphonooxyethyl)thiazole + hydron + 4-amino-2-methyl-5-diphosphomethylpyrimidine → Pyrophosphate + Thiamine monophosphate
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-00mk-9650000000-08bf434ea88992a9a4c2JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0fk9-1985000000-3a09f9d4629fc67167b4JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00di-2910000000-519c49a9a42eb58dbf1eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00di-8920000000-df2ebfff455ef698c727JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0002-0590000000-b75372b224114b47dc78JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9520000000-644ea3121149c231daddJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-2a0a63f471fc524aa92fJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Llorente, B., Fairhead, C., Dujon, B. (1999). "Genetic redundancy and gene fusion in the genome of the Baker's yeast Saccharomyces cerevisiae: functional characterization of a three-member gene family involved in the thiamine biosynthetic pathway." Mol Microbiol 32:1140-1152.10383756
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID16629
HMDB IDNot Available
Pubchem Compound ID217
Kegg IDC04752
ChemSpider ID212
FOODB IDNot Available
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
1. Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase THI21
General function:
Involved in phosphomethylpyrimidine kinase activity
Specific function:
Catalyzes the phosphorylation of hydroxymethylpyrimidine phosphate (HMP-P) to HMP-PP, and also probaby that of HMP to HMP- P
Gene Name:
THI21
Uniprot ID:
Q08975
Molecular weight:
61333.69922
Reactions
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine → ADP + 4-amino-5-phosphonooxymethyl-2-methylpyrimidine.
ATP + 4-amino-2-methyl-5-phosphomethylpyrimidine → ADP + 4-amino-2-methyl-5-diphosphomethylpyrimidine.
Protein Details
2. Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase THI20
General function:
Involved in phosphomethylpyrimidine kinase activity
Specific function:
Catalyzes the phosphorylation of hydroxymethylpyrimidine phosphate (HMP-P) to HMP-PP, and also probaby that of HMP to HMP- P
Gene Name:
THI20
Uniprot ID:
Q08224
Molecular weight:
61268.89844
Reactions
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine → ADP + 4-amino-5-phosphonooxymethyl-2-methylpyrimidine.
ATP + 4-amino-2-methyl-5-phosphomethylpyrimidine → ADP + 4-amino-2-methyl-5-diphosphomethylpyrimidine.
thiamine + H2O → 4-amino-5-hydroxymethyl-2-methylpyrimidine + 5-(2-hydroxyethyl)-4-methylthiazole.
Protein Details
3. Thiamine biosynthetic bifunctional enzyme
General function:
Involved in catalytic activity
Specific function:
Essential for thiamine biosynthesis. The kinase activity is involved in the salvage synthesis of TH-P from the thiazole
Gene Name:
THI6
Uniprot ID:
P41835
Molecular weight:
58058.19922
Reactions
2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate + 4-methyl-5-(2-phosphono-oxyethyl)thiazole → diphosphate + thiamine phosphate.
ATP + 4-methyl-5-(2-hydroxyethyl)thiazole → ADP + 4-methyl-5-(2-phosphonooxyethyl)thiazole.
Protein Details
4. Thiamine biosynthesis protein THI22
General function:
Coenzyme transport and metabolism
Specific function:
Essential for thiamine biosynthesis
Gene Name:
THI22
Uniprot ID:
Q06490
Molecular weight:
63306.39844
Reactions